Multiple sequence alignment - TraesCS1B01G139300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G139300 chr1B 100.000 2411 0 0 1 2411 183211206 183213616 0.000000e+00 4453.0
1 TraesCS1B01G139300 chr3B 98.332 1439 23 1 3 1441 7283121 7281684 0.000000e+00 2523.0
2 TraesCS1B01G139300 chr3B 95.576 972 40 3 1441 2411 166839596 166840565 0.000000e+00 1554.0
3 TraesCS1B01G139300 chr3B 95.946 148 6 0 1294 1441 653680754 653680607 8.610000e-60 241.0
4 TraesCS1B01G139300 chr2D 95.668 1131 49 0 314 1444 413689703 413688573 0.000000e+00 1818.0
5 TraesCS1B01G139300 chr7B 95.679 972 39 3 1441 2411 432881310 432882279 0.000000e+00 1559.0
6 TraesCS1B01G139300 chr7B 95.469 971 42 2 1441 2411 150536174 150535206 0.000000e+00 1548.0
7 TraesCS1B01G139300 chr7B 100.000 56 0 0 1386 1441 495085022 495085077 1.180000e-18 104.0
8 TraesCS1B01G139300 chr7B 95.000 60 3 0 1382 1441 251152462 251152403 7.100000e-16 95.3
9 TraesCS1B01G139300 chr6B 95.469 971 42 2 1441 2411 223098565 223099533 0.000000e+00 1548.0
10 TraesCS1B01G139300 chr6B 95.366 971 43 2 1441 2411 426697485 426698453 0.000000e+00 1543.0
11 TraesCS1B01G139300 chr6B 98.420 633 10 0 809 1441 707945727 707946359 0.000000e+00 1114.0
12 TraesCS1B01G139300 chr6B 73.728 1454 345 34 5 1441 21180222 21181655 3.530000e-148 534.0
13 TraesCS1B01G139300 chr6B 97.222 72 2 0 1370 1441 362196194 362196265 3.260000e-24 122.0
14 TraesCS1B01G139300 chr5B 95.473 972 41 3 1441 2411 112517575 112516606 0.000000e+00 1548.0
15 TraesCS1B01G139300 chr5B 95.469 971 42 2 1441 2411 706440828 706439860 0.000000e+00 1548.0
16 TraesCS1B01G139300 chr2B 95.469 971 43 1 1441 2411 216397109 216398078 0.000000e+00 1548.0
17 TraesCS1B01G139300 chr4B 95.366 971 43 2 1441 2411 440596126 440595158 0.000000e+00 1543.0
18 TraesCS1B01G139300 chr7A 76.168 1456 314 30 3 1441 711304286 711305725 0.000000e+00 736.0
19 TraesCS1B01G139300 chr6A 75.275 1452 329 26 5 1437 469918908 469920348 0.000000e+00 665.0
20 TraesCS1B01G139300 chr6A 81.106 217 37 4 317 531 140031511 140031725 1.150000e-38 171.0
21 TraesCS1B01G139300 chr6A 81.106 217 37 4 317 531 140053653 140053867 1.150000e-38 171.0
22 TraesCS1B01G139300 chr3A 73.697 806 180 26 14 810 37348184 37347402 3.920000e-73 285.0
23 TraesCS1B01G139300 chr4A 92.481 133 10 0 1299 1431 718037960 718038092 8.800000e-45 191.0
24 TraesCS1B01G139300 chr4A 92.481 133 10 0 1299 1431 718143286 718143418 8.800000e-45 191.0
25 TraesCS1B01G139300 chr1D 73.245 527 129 11 317 837 492531434 492530914 5.290000e-42 182.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G139300 chr1B 183211206 183213616 2410 False 4453 4453 100.000 1 2411 1 chr1B.!!$F1 2410
1 TraesCS1B01G139300 chr3B 7281684 7283121 1437 True 2523 2523 98.332 3 1441 1 chr3B.!!$R1 1438
2 TraesCS1B01G139300 chr3B 166839596 166840565 969 False 1554 1554 95.576 1441 2411 1 chr3B.!!$F1 970
3 TraesCS1B01G139300 chr2D 413688573 413689703 1130 True 1818 1818 95.668 314 1444 1 chr2D.!!$R1 1130
4 TraesCS1B01G139300 chr7B 432881310 432882279 969 False 1559 1559 95.679 1441 2411 1 chr7B.!!$F1 970
5 TraesCS1B01G139300 chr7B 150535206 150536174 968 True 1548 1548 95.469 1441 2411 1 chr7B.!!$R1 970
6 TraesCS1B01G139300 chr6B 223098565 223099533 968 False 1548 1548 95.469 1441 2411 1 chr6B.!!$F2 970
7 TraesCS1B01G139300 chr6B 426697485 426698453 968 False 1543 1543 95.366 1441 2411 1 chr6B.!!$F4 970
8 TraesCS1B01G139300 chr6B 707945727 707946359 632 False 1114 1114 98.420 809 1441 1 chr6B.!!$F5 632
9 TraesCS1B01G139300 chr6B 21180222 21181655 1433 False 534 534 73.728 5 1441 1 chr6B.!!$F1 1436
10 TraesCS1B01G139300 chr5B 112516606 112517575 969 True 1548 1548 95.473 1441 2411 1 chr5B.!!$R1 970
11 TraesCS1B01G139300 chr5B 706439860 706440828 968 True 1548 1548 95.469 1441 2411 1 chr5B.!!$R2 970
12 TraesCS1B01G139300 chr2B 216397109 216398078 969 False 1548 1548 95.469 1441 2411 1 chr2B.!!$F1 970
13 TraesCS1B01G139300 chr4B 440595158 440596126 968 True 1543 1543 95.366 1441 2411 1 chr4B.!!$R1 970
14 TraesCS1B01G139300 chr7A 711304286 711305725 1439 False 736 736 76.168 3 1441 1 chr7A.!!$F1 1438
15 TraesCS1B01G139300 chr6A 469918908 469920348 1440 False 665 665 75.275 5 1437 1 chr6A.!!$F3 1432
16 TraesCS1B01G139300 chr3A 37347402 37348184 782 True 285 285 73.697 14 810 1 chr3A.!!$R1 796

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
670 674 1.00358 ACCAATGCACGGATGAGAAGT 59.996 47.619 10.93 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 1843 1.670295 GCATAATCATGTGGACACGCA 59.33 47.619 0.0 0.0 42.06 5.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.102588 GGAGAACAGGTGCGTATATGGT 59.897 50.000 0.00 0.00 0.00 3.55
555 556 1.783071 TGTATAGGTGTCCGATGGCA 58.217 50.000 0.00 0.00 0.00 4.92
647 651 2.360475 GTGGGCTCTTCACCTGCC 60.360 66.667 0.00 0.00 45.42 4.85
667 671 1.811965 CAAACCAATGCACGGATGAGA 59.188 47.619 10.93 0.00 0.00 3.27
670 674 1.003580 ACCAATGCACGGATGAGAAGT 59.996 47.619 10.93 0.00 0.00 3.01
784 788 4.380233 GCAGATTTTTGTGCAGCTACATCT 60.380 41.667 0.00 0.00 39.62 2.90
967 979 1.775039 ATTGAACATCGATGGCGCCG 61.775 55.000 28.09 10.43 37.46 6.46
1124 1136 0.613260 ATTTCCCTCACGCTAGCACA 59.387 50.000 16.45 0.00 0.00 4.57
1469 1482 4.826733 TGAAAAGAATGCTTTAGGTGCTGA 59.173 37.500 0.00 0.00 43.32 4.26
1501 1514 8.735692 TGTTGAATTCATTCATGATGCTACTA 57.264 30.769 9.40 0.00 45.30 1.82
1561 1574 9.822185 GGAATTGCAATAATATCAAGTTTCCTT 57.178 29.630 13.39 0.00 31.31 3.36
1793 1806 3.838120 AGGCATTAAAGAAAAGCGCTTC 58.162 40.909 25.24 12.58 0.00 3.86
1800 1813 1.239347 AGAAAAGCGCTTCTTGGGAC 58.761 50.000 25.24 9.64 34.67 4.46
1902 1915 9.606631 TTTTGTTTCAATAAAGTGCCAAGTAAT 57.393 25.926 0.00 0.00 0.00 1.89
1945 1958 5.419542 GTGATAGTTGTGTTGATCCTGCTA 58.580 41.667 0.00 0.00 0.00 3.49
1965 1978 7.172019 CCTGCTAAAAATCAGAAACTTTTGCAT 59.828 33.333 9.91 0.00 31.79 3.96
2316 2332 4.232221 CGGAGCTTACGAGTTTTCTGTTA 58.768 43.478 5.93 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.490490 ACACGCCACATGATCCCTTAT 59.510 47.619 0.00 0.00 0.00 1.73
1 2 0.908910 ACACGCCACATGATCCCTTA 59.091 50.000 0.00 0.00 0.00 2.69
49 50 1.008327 TCTAGGGAGCCAAGGATCACA 59.992 52.381 9.55 0.00 36.23 3.58
539 540 2.799126 TTTTGCCATCGGACACCTAT 57.201 45.000 0.00 0.00 0.00 2.57
647 651 1.811965 TCTCATCCGTGCATTGGTTTG 59.188 47.619 7.71 7.34 0.00 2.93
667 671 2.567169 TCATGATCACCGGAAGACACTT 59.433 45.455 9.46 0.00 0.00 3.16
670 674 1.135112 CGTCATGATCACCGGAAGACA 60.135 52.381 9.46 7.35 0.00 3.41
967 979 0.467804 GTGCCATCCTCTTCTCTCCC 59.532 60.000 0.00 0.00 0.00 4.30
1124 1136 3.097614 AGGATAAACGGCAGTGTAGTCT 58.902 45.455 0.00 0.00 0.00 3.24
1352 1365 3.640029 GCCAATTTCATCAGGTCCATGAT 59.360 43.478 0.00 0.00 40.59 2.45
1561 1574 6.371548 AGCTTCACGAATTTAAGCACATAGAA 59.628 34.615 14.31 0.00 46.35 2.10
1800 1813 8.519799 ACAGTAAGGATAAATATTGGGTTGTG 57.480 34.615 0.00 0.00 0.00 3.33
1830 1843 1.670295 GCATAATCATGTGGACACGCA 59.330 47.619 0.00 0.00 42.06 5.24
1831 1844 1.942657 AGCATAATCATGTGGACACGC 59.057 47.619 0.00 0.00 34.40 5.34
1832 1845 4.209911 CAGTAGCATAATCATGTGGACACG 59.790 45.833 0.00 0.00 34.40 4.49
1902 1915 4.467082 TCACCGTAAGCCATCCTAAAGTTA 59.533 41.667 0.00 0.00 0.00 2.24
1904 1917 2.835764 TCACCGTAAGCCATCCTAAAGT 59.164 45.455 0.00 0.00 0.00 2.66
1945 1958 7.049754 ACTGGATGCAAAAGTTTCTGATTTTT 58.950 30.769 0.00 0.00 0.00 1.94
2114 2128 7.979444 ACAGAATCTATCAAAAACGGAAGAA 57.021 32.000 0.00 0.00 0.00 2.52
2242 2258 9.522804 CTTAGGTACTGTAATGAACTCATTCTC 57.477 37.037 8.19 4.84 42.19 2.87
2316 2332 7.494298 ACTTGAAAACTTCACAACACAAAACTT 59.506 29.630 0.00 0.00 39.87 2.66


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.